Resources
Deuteros is a MATLAB based tool for data analysis and visualisation of differential data from hydrogen deuterium exchange mass spectrometry (HDX-MS). Deuteros takes as input, mass assigned peptide lists from DynamX (Waters Corp.) software, performs statistical filtering of peptides to identify those with significantly altered uptake, produces a myriad of data plots including Woods plots, and outputs PyMOL-compatible scripts for visualisation on molecular structures. Deuteros is available from the Github repository here. See also the associated publication here.
IMPACT (Ion Mobility Projection Approximation Calculation Tool) developed by the Benesch group (Oxford University) is a program that can calculate the theoretical collision cross-section (CCS) of protein models through the projection approximation method. Calculations can also be made on coordinate trajectory files produced from popular molecular dynamic simulation packages such as GROMACS, allowing per-frame CCS measurements to be calculated in a high-throughput manner. IMPACT is available to download here as a standalone command-line executable and can be run on Unix-based operating systems. The publication for IMPACT can be found here.
MOBCAL is a molecular calculator for theoretical collision cross-section of molecular structures. Calculations can be made through either the projection approximation, exact hard sphere scattering, or trajectory methods. MOBCAL is freely available here from the MFJ group at Indiana University, as a command-line tool for Unix-based operating systems.
PULSAR
PULSAR is a gui program developed within the Robinson group (Oxford University) for analysing data sourced from ion-mobility mass spectrometry. PULSAR allows the visualisation of mobility data and can calculate the experimental collision cross-section of ions (for both linear and T-wave assisted ion-mobility). The software is currently only available for Windows-based operating systems and can be found here.